HEADER TRANSCRIPTION 24-FEB-22 7Z1K TITLE CRYSTAL STRUCTURE OF THE SPOC DOMAIN OF HUMAN SHARP (SPEN) IN COMPLEX TITLE 2 WITH RNA POLYMERASE II CTD HEPTAPEPTIDE PHOSPHORYLATED ON SER5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MSX2-INTERACTING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SMART/HDAC1-ASSOCIATED REPRESSOR PROTEIN,SPEN HOMOLOG; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: SER-TYR-SER-PRO-THR-SEP; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SPEN, KIAA0929, MINT, SHARP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS HUMAN SHARP, SPOC DOMAIN, RNA POLYMERASE II CTD HEPTAPEPTIDE, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR L.APPEL,I.GRISHKOVSKAYA,D.SLADE,K.DJINOVIC-CARUGO REVDAT 3 07-FEB-24 7Z1K 1 REMARK REVDAT 2 25-JAN-23 7Z1K 1 JRNL REVDAT 1 07-DEC-22 7Z1K 0 JRNL AUTH L.M.APPEL,V.FRANKE,J.BENEDUM,I.GRISHKOVSKAYA,X.STROBL, JRNL AUTH 2 A.POLYANSKY,G.AMMANN,S.PLATZER,A.NEUDOLT,A.WUNDER,L.WALCH, JRNL AUTH 3 S.KAISER,B.ZAGROVIC,K.DJINOVIC-CARUGO,A.AKALIN,D.SLADE JRNL TITL THE SPOC DOMAIN IS A PHOSPHOSERINE BINDING MODULE THAT JRNL TITL 2 BRIDGES TRANSCRIPTION MACHINERY WITH CO- AND JRNL TITL 3 POST-TRANSCRIPTIONAL REGULATORS. JRNL REF NAT COMMUN V. 14 166 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36631525 JRNL DOI 10.1038/S41467-023-35853-1 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26220 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1331 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.2300 - 3.3400 0.98 2647 138 0.1726 0.1997 REMARK 3 2 3.3400 - 2.6500 1.00 2579 128 0.1890 0.2427 REMARK 3 3 2.6500 - 2.3200 1.00 2540 132 0.1998 0.2107 REMARK 3 4 2.3200 - 2.1000 0.98 2469 138 0.2191 0.2505 REMARK 3 5 2.1000 - 1.9500 0.98 2485 116 0.2348 0.2518 REMARK 3 6 1.9500 - 1.8400 0.98 2441 143 0.3620 0.4223 REMARK 3 7 1.8400 - 1.7500 0.99 2485 139 0.3951 0.3757 REMARK 3 8 1.7500 - 1.6700 0.99 2478 134 0.3492 0.3800 REMARK 3 9 1.6700 - 1.6100 0.98 2433 137 0.3403 0.3780 REMARK 3 10 1.6100 - 1.5500 0.94 2332 126 0.3494 0.3365 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.255 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.615 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1329 REMARK 3 ANGLE : 0.731 1814 REMARK 3 CHIRALITY : 0.047 216 REMARK 3 PLANARITY : 0.008 233 REMARK 3 DIHEDRAL : 7.897 186 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7Z1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1292121371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9660 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26393 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 36.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1OW1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M POTASSIUM THIOCYANATE, 30% W/V REMARK 280 PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.66350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.13650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.25850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.13650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.66350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.25850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 3493 REMARK 465 ALA A 3494 REMARK 465 MET A 3495 REMARK 465 VAL A 3496 REMARK 465 ASP A 3497 REMARK 465 MET A 3498 REMARK 465 VAL A 3499 REMARK 465 PRO B -2 REMARK 465 PRO B 5 REMARK 465 SER B 6 REMARK 465 TYR B 7 REMARK 465 SER B 8 REMARK 465 PRO B 9 REMARK 465 THR B 10 REMARK 465 SER B 11 REMARK 465 PRO B 12 REMARK 465 SER B 13 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A3500 CG CD OE1 NE2 REMARK 470 GLU A3542 CG CD OE1 OE2 REMARK 470 ASN A3652 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 3761 O HOH A 3765 2.10 REMARK 500 O HOH A 3786 O HOH A 3801 2.12 REMARK 500 O GLN A 3621 O HOH A 3701 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A3516 -125.94 57.66 REMARK 500 ASN A3652 14.40 57.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 7Z1K A 3496 3664 UNP Q96T58 MINT_HUMAN 3496 3664 DBREF 7Z1K B -2 13 PDB 7Z1K 7Z1K -2 13 SEQADV 7Z1K GLY A 3493 UNP Q96T58 EXPRESSION TAG SEQADV 7Z1K ALA A 3494 UNP Q96T58 EXPRESSION TAG SEQADV 7Z1K MET A 3495 UNP Q96T58 EXPRESSION TAG SEQRES 1 A 172 GLY ALA MET VAL ASP MET VAL GLN LEU LEU LYS LYS TYR SEQRES 2 A 172 PRO ILE VAL TRP GLN GLY LEU LEU ALA LEU LYS ASN ASP SEQRES 3 A 172 THR ALA ALA VAL GLN LEU HIS PHE VAL SER GLY ASN ASN SEQRES 4 A 172 VAL LEU ALA HIS ARG SER LEU PRO LEU SER GLU GLY GLY SEQRES 5 A 172 PRO PRO LEU ARG ILE ALA GLN ARG MET ARG LEU GLU ALA SEQRES 6 A 172 THR GLN LEU GLU GLY VAL ALA ARG ARG MET THR VAL GLU SEQRES 7 A 172 THR ASP TYR CYS LEU LEU LEU ALA LEU PRO CYS GLY ARG SEQRES 8 A 172 ASP GLN GLU ASP VAL VAL SER GLN THR GLU SER LEU LYS SEQRES 9 A 172 ALA ALA PHE ILE THR TYR LEU GLN ALA LYS GLN ALA ALA SEQRES 10 A 172 GLY ILE ILE ASN VAL PRO ASN PRO GLY SER ASN GLN PRO SEQRES 11 A 172 ALA TYR VAL LEU GLN ILE PHE PRO PRO CYS GLU PHE SER SEQRES 12 A 172 GLU SER HIS LEU SER ARG LEU ALA PRO ASP LEU LEU ALA SEQRES 13 A 172 SER ILE SER ASN ILE SER PRO HIS LEU MET ILE VAL ILE SEQRES 14 A 172 ALA SER VAL SEQRES 1 B 16 PRO SER TYR SER PRO THR SEP PRO SER TYR SER PRO THR SEQRES 2 B 16 SER PRO SER HET SEP B 4 10 HETNAM SEP PHOSPHOSERINE HETSYN SEP PHOSPHONOSERINE FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 HOH *169(H2 O) HELIX 1 AA1 ASN A 3531 LEU A 3538 1 8 HELIX 2 AA2 GLU A 3556 ARG A 3566 1 11 HELIX 3 AA3 ASP A 3584 PHE A 3599 1 16 HELIX 4 AA4 PHE A 3599 GLN A 3607 1 9 HELIX 5 AA5 CYS A 3632 ALA A 3643 1 12 HELIX 6 AA6 ALA A 3643 SER A 3651 1 9 SHEET 1 AA1 9 LEU A3547 ILE A3549 0 SHEET 2 AA1 9 ILE A3507 LEU A3515 1 N ALA A3514 O ILE A3549 SHEET 3 AA1 9 ASP A3518 GLY A3529 -1 O LEU A3524 N TRP A3509 SHEET 4 AA1 9 TYR A3573 PRO A3580 -1 O LEU A3577 N HIS A3525 SHEET 5 AA1 9 LEU A3657 SER A3663 -1 O ILE A3661 N CYS A3574 SHEET 6 AA1 9 PRO A3622 PHE A3629 -1 N PHE A3629 O MET A3658 SHEET 7 AA1 9 ALA A3608 PRO A3615 -1 N VAL A3614 O TYR A3624 SHEET 8 AA1 9 GLN A3551 ARG A3554 -1 N MET A3553 O ALA A3609 SHEET 9 AA1 9 SER B 1 PRO B 2 -1 O SER B 1 N ARG A3552 LINK C THR B 3 N SEP B 4 1555 1555 1.33 CRYST1 43.327 60.517 68.273 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.023080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016524 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014647 0.00000